Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: XQNVY

Calculation Name: 4GMQ-A-Xray29

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GMQ

Chain ID: A

ChEMBL ID:

UniProt ID: G0RYD6

Base Structure: X-ray

Registration Date: 2018-09-06

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -792705.24795
FMO2-HF: Nuclear repulsion 752192.83539
FMO2-HF: Total energy -40512.41256
FMO2-MP2: Total energy -40630.81125


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:354:ACE)


Summations of interaction energy for fragment #1(A:354:ACE)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-3.526-7.513.209-6.091-3.1440.008
Interaction energy analysis for fragmet #1(A:354:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.029
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A356ALA00.1090.0483.7580.5451.659-0.021-0.475-0.617-0.001
4A357VAL00.1100.0636.1600.2730.2730.0000.0000.0000.000
5A358LYS10.8330.9541.753-5.200-10.49313.227-5.539-2.3950.009
6A359LYS10.8950.9335.0691.1771.235-0.001-0.009-0.0480.000
7A360ASN00.0870.0397.3010.1500.1500.0000.0000.0000.000
8A361LYS10.9370.9777.375-0.184-0.1840.0000.0000.0000.000
9A362ARG10.8150.8986.301-0.804-0.8040.0000.0000.0000.000
10A363VAL00.0140.03010.6310.0040.0040.0000.0000.0000.000
11A364LEU00.0150.01913.1610.0130.0130.0000.0000.0000.000
12A365ARG10.8880.94210.296-0.262-0.2620.0000.0000.0000.000
13A366GLY00.0000.00414.5260.0030.0030.0000.0000.0000.000
14A367SER00.0020.00016.224-0.010-0.0100.0000.0000.0000.000
15A368VAL00.0600.02718.942-0.004-0.0040.0000.0000.0000.000
16A369LYS10.9000.96019.272-0.126-0.1260.0000.0000.0000.000
17A370GLU-1-0.912-0.93620.4450.0440.0440.0000.0000.0000.000
18A371ALA00.0060.01222.181-0.006-0.0060.0000.0000.0000.000
19A372ASN0-0.028-0.01024.4240.0050.0050.0000.0000.0000.000
20A373TYR0-0.006-0.00720.6440.0020.0020.0000.0000.0000.000
21A374PHE0-0.017-0.01223.559-0.001-0.0010.0000.0000.0000.000
22A375VAL0-0.0210.02228.301-0.004-0.0040.0000.0000.0000.000
23A376GLU-1-0.806-0.88030.6840.0300.0300.0000.0000.0000.000
24A377GLY0-0.026-0.01133.2210.0020.0020.0000.0000.0000.000
25A378GLU-1-0.961-0.97130.0600.0770.0770.0000.0000.0000.000
26A379ALA00.0050.01227.090-0.002-0.0020.0000.0000.0000.000
27A380SER0-0.009-0.04028.7680.0070.0070.0000.0000.0000.000
28A381ALA00.028-0.01326.9320.0040.0040.0000.0000.0000.000
29A382ALA00.0240.01226.7720.0050.0050.0000.0000.0000.000
30A383THR00.0390.03627.231-0.003-0.0030.0000.0000.0000.000
31A384ILE00.0080.00122.2980.0010.0010.0000.0000.0000.000
32A385ASP-1-0.818-0.89023.1080.1150.1150.0000.0000.0000.000
33A386ALA0-0.009-0.00523.5610.0010.0010.0000.0000.0000.000
34A387VAL00.0300.01122.108-0.003-0.0030.0000.0000.0000.000
35A388LEU0-0.020-0.01517.494-0.001-0.0010.0000.0000.0000.000
36A389ASN0-0.012-0.00319.3270.0170.0170.0000.0000.0000.000
37A390ASP-1-0.694-0.81521.0650.0480.0480.0000.0000.0000.000
38A391VAL0-0.034-0.01116.435-0.008-0.0080.0000.0000.0000.000
39A392ASP-1-0.813-0.89215.9180.1850.1850.0000.0000.0000.000
40A393LEU00.0230.02017.272-0.007-0.0070.0000.0000.0000.000
41A394VAL00.0690.04018.546-0.013-0.0130.0000.0000.0000.000
42A395ILE0-0.020-0.00912.722-0.015-0.0150.0000.0000.0000.000
43A396THR0-0.113-0.05415.396-0.021-0.0210.0000.0000.0000.000
44A397LYS10.9080.96316.877-0.029-0.0290.0000.0000.0000.000
45A398ILE0-0.0150.02715.531-0.016-0.0160.0000.0000.0000.000
46A399ASP-1-0.717-0.83814.789-0.181-0.1810.0000.0000.0000.000
47A400ALA00.006-0.02111.008-0.012-0.0120.0000.0000.0000.000
48A401ASP-1-0.798-0.88612.534-0.346-0.3460.0000.0000.0000.000
49A402GLU-1-0.712-0.84615.471-0.089-0.0890.0000.0000.0000.000
50A403ILE0-0.012-0.00411.0710.0120.0120.0000.0000.0000.000
51A404ALA0-0.031-0.02012.9280.0100.0100.0000.0000.0000.000
52A405ALA0-0.0070.00514.0460.0210.0210.0000.0000.0000.000
53A406LEU00.0470.02816.8340.0130.0130.0000.0000.0000.000
54A407ALA00.006-0.01613.6710.0170.0170.0000.0000.0000.000
55A408GLY0-0.040-0.02015.7040.0130.0130.0000.0000.0000.000
56A409LYS10.9370.99817.9180.1100.1100.0000.0000.0000.000
57A410LEU00.0560.03617.5520.0110.0110.0000.0000.0000.000
58A411ASN0-0.044-0.00715.2510.0330.0330.0000.0000.0000.000
59A412GLY00.0640.04718.564-0.007-0.0070.0000.0000.0000.000
60A413LEU0-0.0080.04221.2370.0060.0060.0000.0000.0000.000
61A414THR00.0420.01322.8370.0070.0070.0000.0000.0000.000
62A415VAL00.0250.02825.4890.0080.0080.0000.0000.0000.000
63A416ALA00.0720.02826.530-0.002-0.0020.0000.0000.0000.000
64A417ASP-1-0.709-0.79527.2830.0120.0120.0000.0000.0000.000
65A418GLU-1-0.826-0.84326.942-0.026-0.0260.0000.0000.0000.000
66A419ILE0-0.002-0.01422.148-0.006-0.0060.0000.0000.0000.000
67A420LYS10.8000.88624.302-0.028-0.0280.0000.0000.0000.000
68A421ASN0-0.003-0.00926.4450.0010.0010.0000.0000.0000.000
69A422VAL0-0.0110.01621.830-0.005-0.0050.0000.0000.0000.000
70A423TRP00.007-0.02017.288-0.007-0.0070.0000.0000.0000.000
71A424LYS10.8720.94423.717-0.008-0.0080.0000.0000.0000.000
72A425GLU-1-0.822-0.86825.992-0.042-0.0420.0000.0000.0000.000
73A426GLU-1-0.756-0.85920.264-0.072-0.0720.0000.0000.0000.000
74A427VAL00.002-0.00523.944-0.001-0.0010.0000.0000.0000.000
75A428SER00.0220.02025.5350.0010.0010.0000.0000.0000.000
76A429ARG10.7670.87820.8650.0720.0720.0000.0000.0000.000
77A430LEU0-0.024-0.02621.135-0.002-0.0020.0000.0000.0000.000
78A431VAL00.0010.00825.5250.0010.0010.0000.0000.0000.000
79A432GLY00.0180.01828.9050.0010.0010.0000.0000.0000.000
80A433ALA0-0.044-0.01026.309-0.002-0.0020.0000.0000.0000.000
81A434GLY0-0.0060.01928.377-0.002-0.0020.0000.0000.0000.000
82A435LYS10.7890.88821.8370.0710.0710.0000.0000.0000.000
83A436LEU0-0.0120.00423.4240.0070.0070.0000.0000.0000.000
84A437LYS10.9290.95926.890-0.001-0.0010.0000.0000.0000.000
85A438GLU-1-0.891-0.92929.8350.0060.0060.0000.0000.0000.000
86A439GLY00.0130.00131.2570.0010.0010.0000.0000.0000.000
87A440ASP-1-0.892-0.91726.5480.0250.0250.0000.0000.0000.000
88A441ILE0-0.058-0.01723.4870.0080.0080.0000.0000.0000.000
89A442LYS10.8670.95625.642-0.068-0.0680.0000.0000.0000.000
90A443ALA00.003-0.00627.074-0.003-0.0030.0000.0000.0000.000
91A444LEU0-0.039-0.02722.026-0.002-0.0020.0000.0000.0000.000
92A445VAL00.010-0.00826.100-0.005-0.0050.0000.0000.0000.000
93A446ALA-1-0.759-0.82628.8690.0130.0130.0000.0000.0000.000
94A501HOH00.000-0.00419.4160.0050.0050.0000.0000.0000.000
95A503HOH00.0110.00410.539-0.006-0.0060.0000.0000.0000.000
96A504HOH0-0.036-0.02418.685-0.002-0.0020.0000.0000.0000.000
97A505HOH0-0.036-0.02210.919-0.032-0.0320.0000.0000.0000.000
98A506HOH0-0.043-0.03623.598-0.002-0.0020.0000.0000.0000.000
99A507HOH0-0.024-0.0197.0320.0050.0050.0000.0000.0000.000
100A508HOH00.0120.0098.7140.0600.0600.0000.0000.0000.000
101A509HOH0-0.040-0.03628.477-0.002-0.0020.0000.0000.0000.000
102A510HOH0-0.017-0.01716.5380.0090.0090.0000.0000.0000.000
103A511HOH0-0.034-0.02520.551-0.002-0.0020.0000.0000.0000.000
104A512HOH0-0.030-0.01919.5240.0050.0050.0000.0000.0000.000
105A514HOH0-0.049-0.04730.4480.0010.0010.0000.0000.0000.000
106A515HOH00.0030.00010.1580.0290.0290.0000.0000.0000.000
107A516HOH00.0190.01625.4680.0000.0000.0000.0000.0000.000
108A517HOH0-0.025-0.01527.4860.0000.0000.0000.0000.0000.000
109A519HOH0-0.023-0.02020.529-0.004-0.0040.0000.0000.0000.000
110A520HOH0-0.052-0.04228.8610.0010.0010.0000.0000.0000.000
111A521HOH0-0.051-0.03130.7330.0020.0020.0000.0000.0000.000
112A523HOH00.008-0.00222.941-0.001-0.0010.0000.0000.0000.000
113A524HOH00.0250.00829.9500.0010.0010.0000.0000.0000.000
114A525HOH0-0.003-0.00523.6890.0020.0020.0000.0000.0000.000
115A526HOH0-0.025-0.01914.8570.0090.0090.0000.0000.0000.000
116A527HOH0-0.068-0.04713.199-0.017-0.0170.0000.0000.0000.000
117A528HOH00.0220.00127.1390.0020.0020.0000.0000.0000.000
118A530HOH0-0.044-0.02134.9980.0000.0000.0000.0000.0000.000
119A531HOH00.0130.00820.772-0.002-0.0020.0000.0000.0000.000
120A532HOH00.0270.01329.9290.0020.0020.0000.0000.0000.000
121A533HOH0-0.010-0.00428.386-0.002-0.0020.0000.0000.0000.000
122A534HOH0-0.025-0.01821.1160.0050.0050.0000.0000.0000.000
123A535HOH0-0.020-0.01516.2120.0010.0010.0000.0000.0000.000
124A536HOH0-0.037-0.03219.5290.0020.0020.0000.0000.0000.000
125A537HOH0-0.056-0.05128.4210.0010.0010.0000.0000.0000.000
126A540HOH00.0440.0298.7930.0640.0640.0000.0000.0000.000
127A541HOH0-0.045-0.02820.3510.0050.0050.0000.0000.0000.000
128A542HOH0-0.060-0.05432.359-0.001-0.0010.0000.0000.0000.000
129A543HOH00.0160.00031.1500.0020.0020.0000.0000.0000.000
130A544HOH00.0210.01814.2080.0030.0030.0000.0000.0000.000
131A545HOH0-0.032-0.03029.323-0.002-0.0020.0000.0000.0000.000
132A546HOH0-0.013-0.00427.0850.0010.0010.0000.0000.0000.000
133A548HOH0-0.025-0.01825.750-0.002-0.0020.0000.0000.0000.000
134A549HOH0-0.002-0.00629.4540.0020.0020.0000.0000.0000.000
135A550HOH0-0.061-0.03415.603-0.018-0.0180.0000.0000.0000.000
136A552HOH0-0.038-0.02926.0990.0010.0010.0000.0000.0000.000
137A553HOH0-0.044-0.02415.933-0.012-0.0120.0000.0000.0000.000
138A556HOH00.0120.00929.384-0.002-0.0020.0000.0000.0000.000
139A557HOH00.0190.01531.6030.0010.0010.0000.0000.0000.000
140A558HOH0-0.087-0.10234.029-0.001-0.0010.0000.0000.0000.000
141A562HOH0-0.005-0.00115.150-0.013-0.0130.0000.0000.0000.000
142A563HOH0-0.046-0.04423.710-0.002-0.0020.0000.0000.0000.000
143A566HOH0-0.007-0.00727.6020.0020.0020.0000.0000.0000.000
144A568HOH00.0510.0263.8930.5850.6740.004-0.048-0.0460.000
145A569HOH00.0090.00230.7440.0000.0000.0000.0000.0000.000
146A570HOH0-0.039-0.02827.0690.0030.0030.0000.0000.0000.000
147A571HOH0-0.082-0.06028.211-0.002-0.0020.0000.0000.0000.000
148A572HOH00.013-0.0084.927-0.129-0.1290.0000.0000.0000.000
149A573HOH00.017-0.00526.437-0.001-0.0010.0000.0000.0000.000
150A574HOH0-0.041-0.03232.9920.0010.0010.0000.0000.0000.000
151A575HOH0-0.054-0.06829.9260.0020.0020.0000.0000.0000.000
152A576HOH00.0280.01634.5360.0020.0020.0000.0000.0000.000
153A581HOH0-0.042-0.04724.6810.0030.0030.0000.0000.0000.000
154A582HOH00.0370.01710.258-0.052-0.0520.0000.0000.0000.000
155A584HOH0-0.043-0.03232.108-0.002-0.0020.0000.0000.0000.000
156A588HOH00.0340.0236.7410.0450.0450.0000.0000.0000.000
157A589HOH0-0.042-0.02618.3250.0060.0060.0000.0000.0000.000
158A591HOH0-0.068-0.04918.4560.0080.0080.0000.0000.0000.000
159A592HOH00.0160.00719.138-0.005-0.0050.0000.0000.0000.000
160A595HOH00.0450.02630.8240.0000.0000.0000.0000.0000.000
161A596HOH0-0.026-0.01521.164-0.004-0.0040.0000.0000.0000.000
162A597HOH0-0.054-0.02915.4600.0200.0200.0000.0000.0000.000
163A599HOH00.0250.01322.8200.0020.0020.0000.0000.0000.000
164A600HOH0-0.005-0.02021.9920.0030.0030.0000.0000.0000.000
165A604HOH0-0.038-0.02832.7050.0000.0000.0000.0000.0000.000
166A606HOH00.0500.06433.1580.0020.0020.0000.0000.0000.000
167A607HOH0-0.031-0.02221.7290.0060.0060.0000.0000.0000.000
168A609HOH0-0.009-0.00916.898-0.010-0.0100.0000.0000.0000.000
169A614HOH00.0250.02226.872-0.002-0.0020.0000.0000.0000.000
170A616HOH0-0.049-0.05116.3290.0030.0030.0000.0000.0000.000
171A620HOH0-0.033-0.02832.628-0.001-0.0010.0000.0000.0000.000
172A622HOH0-0.054-0.04827.461-0.003-0.0030.0000.0000.0000.000
173A624HOH0-0.071-0.05025.3240.0000.0000.0000.0000.0000.000
174A625HOH0-0.040-0.02631.438-0.001-0.0010.0000.0000.0000.000
175A629HOH0-0.026-0.01622.6710.0030.0030.0000.0000.0000.000
176A638HOH00.0020.0083.9980.3440.4020.000-0.020-0.0380.000
177A642HOH0-0.049-0.03226.997-0.003-0.0030.0000.0000.0000.000
178A646HOH00.0150.00530.4290.0000.0000.0000.0000.0000.000
179A653HOH00.0600.03010.8980.0090.0090.0000.0000.0000.000
180A658HOH0-0.027-0.00814.349-0.002-0.0020.0000.0000.0000.000
181A664HOH00.0070.03921.610-0.004-0.0040.0000.0000.0000.000
182A666HOH0-0.055-0.03530.9790.0010.0010.0000.0000.0000.000
183A675HOH0-0.044-0.04217.861-0.002-0.0020.0000.0000.0000.000
184A678HOH0-0.108-0.12021.042-0.001-0.0010.0000.0000.0000.000